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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
HPS3
HPS3 biogenesis of lysosomal organelles complex 2 subunit 1
Chromosome 3 Β· 3q24
NCBI Gene: 84343Ensembl: ENSG00000163755.10HGNC: HGNC:15597UniProt: G5E9V4
40PubMed Papers
21Diseases
0Drugs
280Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
BLOC-2 complexprotein bindingcytoplasmpigmentationHermansky-Pudlak syndrome 3Hermansky-Pudlak syndromeHermansky-Pudlak syndrome without pulmonary fibrosispreeclampsia
✦AI Summary

HPS3 encodes a 113.7 kDa protein that functions as a component of the BLOC-2 (biogenesis of lysosome-related organelles complex-2) and is critical for early-stage melanosome biogenesis and platelet dense granule formation 1. As part of the BLOC-2 complex, HPS3 is required for proper trafficking and maturation of lysosome-related organelles (LROs), with evidence suggesting it facilitates transport of proteins like the zinc transporter TMEM163 to dense granule precursor compartments 2. Mutations in HPS3 cause Hermansky-Pudlak syndrome type 3 (HPS-3), an autosomal recessive disorder characterized by oculocutaneous albinism and bleeding diathesis due to defective platelet dense bodies and melanosomes 3. HPS-3 typically presents with mild hypopigmentation and prolonged bleeding time, with generally milder systemic manifestations compared to other HPS types, though some patients may develop enterocolitis 14. The condition has been identified across diverse populations, with notably high prevalence in Ashkenazi Jewish communities (estimated 1:200 frequency for one splice site variant) and increasing recognition in Asian and Pakistani populations, indicating broader genetic heterogeneity than initially appreciated 564. Animal models confirm HPS3's role in pigmentation, as mutations produce brown coat color phenotypes in mice and dogs 7.

Sources cited
1
HPS3 codes for a 113.7 kDa protein involved in melanosome and platelet dense body formation; HPS-3 manifests with mild hypopigmentation and bleeding
PMID: 12125811
2
HPS is a group of autosomal recessive disorders with components of four protein complexes including BLOC-2; all HPS individuals exhibit albinism and bleeding diathesis
PMID: 31898847
3
BLOC-2 (Hps6)-deficient and HPS3 patients show reduced TMEM163 levels and platelet dense granule defects; BLOC-1 is required for trafficking of TMEM163 to dense granule precursors
PMID: 33513603
4
HPS-3 presents with oculocutaneous albinism and bleeding diathesis; novel HPS3 deletion mutations identified in Ashkenazi Jewish population
PMID: 36046236
5
HPS, the most common syndromic OCA, is characterized by bleeding tendency and systemic comorbidities; HPS3 identified as rare OCA subtype in Japanese patients
PMID: 32969595
6
HPS-3 presents with oculocutaneous albinism, poor vision, nystagmus, and bleeding diathesis; novel HPS3 nonsense variants identified in Pakistani population
PMID: 36672886
7
HPS3 encodes a protein required for correct biogenesis of lysosome-related organelles including melanosomes; mutations in HPS3 cause mild oculocutaneous albinism and prolonged bleeding
PMID: 32526956
Disease Associationsβ“˜21
Hermansky-Pudlak syndrome 3Open Targets
0.80Strong
Hermansky-Pudlak syndromeOpen Targets
0.70Moderate
Hermansky-Pudlak syndrome without pulmonary fibrosisOpen Targets
0.38Weak
preeclampsiaOpen Targets
0.27Weak
alcohol drinkingOpen Targets
0.26Weak
Hermansky-Pudlak syndrome 2Open Targets
0.26Weak
genetic disorderOpen Targets
0.19Weak
aceruloplasminemiaOpen Targets
0.19Weak
Abnormal bleedingOpen Targets
0.11Weak
Familial prostate cancerOpen Targets
0.11Weak
prostate cancerOpen Targets
0.11Weak
ThrombocytopeniaOpen Targets
0.11Weak
Griscelli diseaseOpen Targets
0.10Weak
Griscelli disease type 3Open Targets
0.10Weak
Griscelli syndrome type 3Open Targets
0.10Weak
Microcephaly - albinism - digital anomaliesOpen Targets
0.09Suggestive
microcephaly-albinism-digital anomalies syndromeOpen Targets
0.09Suggestive
uncombable hair syndromeOpen Targets
0.09Suggestive
X-linked intellectual disability-retinitis pigmentosa syndromeOpen Targets
0.08Suggestive
ringed hair diseaseOpen Targets
0.08Suggestive
Hermansky-Pudlak syndrome 3UniProt
Pathogenic Variants280
NM_032383.5(HPS3):c.1838C>G (p.Ser613Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2026β†’ Residue 613
NM_032383.5(HPS3):c.2424del (p.Ile807_Trp808insTer)Pathogenic
Hermansky-Pudlak syndrome 3|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 807
NM_032383.5(HPS3):c.2507T>G (p.Leu836Ter)Pathogenic
Hermansky-Pudlak syndrome 3|not provided|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 836
NM_032383.5(HPS3):c.2589+1G>APathogenic
not provided|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2026
NM_032383.5(HPS3):c.1870G>T (p.Glu624Ter)Pathogenic
Hermansky-Pudlak syndrome 2|not provided|Hermansky-Pudlak syndrome|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 624
NM_032383.5(HPS3):c.1385C>A (p.Ser462Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 462
NM_032383.5(HPS3):c.1861G>T (p.Glu621Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 621
NM_032383.5(HPS3):c.1189C>T (p.Arg397Trp)Pathogenic
Hermansky-Pudlak syndrome 3|not provided|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 397
NM_032383.5(HPS3):c.1588C>T (p.Arg530Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 530
NM_032383.5(HPS3):c.2464C>T (p.Arg822Ter)Pathogenic
Hermansky-Pudlak syndrome 3|not provided|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 822
NM_032383.5(HPS3):c.2589+1G>CPathogenic
Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome|not provided
β˜…β˜…β˜†β˜†2025
NM_032383.5(HPS3):c.655G>T (p.Glu219Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 219
NM_032383.5(HPS3):c.2208_2209del (p.Gln737fs)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 737
NM_032383.5(HPS3):c.2463dup (p.Arg822fs)Pathogenic
Hermansky-Pudlak syndrome|not provided|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2025β†’ Residue 822
NM_032383.5(HPS3):c.1686C>A (p.Tyr562Ter)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 562
NM_032383.5(HPS3):c.1509+1G>ALikely pathogenic
not provided|Hermansky-Pudlak syndrome 3
β˜…β˜…β˜†β˜†2025
NM_032383.5(HPS3):c.1682_1683del (p.Cys561fs)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 561
NM_032383.5(HPS3):c.2398_2399del (p.Phe800fs)Pathogenic
Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 800
NM_032383.5(HPS3):c.1163+1G>APathogenic
Hermansky-Pudlak syndrome 3|not provided|Hermansky-Pudlak syndrome|HPS3-related disorder
β˜…β˜…β˜†β˜†2025
NM_032383.5(HPS3):c.248dup (p.Asn83fs)Pathogenic
not provided|Hermansky-Pudlak syndrome 3|Hermansky-Pudlak syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 83
View on ClinVar β†—
Related Genes
BLOC1S1Protein interaction100%TYRP1Protein interaction100%SNAPINProtein interaction100%BLOC1S4Protein interaction100%BLOC1S5Protein interaction100%LYSTProtein interaction93%
Tissue Expression6 tissues
Ovary
100%
Brain
96%
Liver
89%
Lung
86%
Bone Marrow
70%
Heart
70%
Gene Interaction Network
Click a node to explore
HPS3BLOC1S1TYRP1SNAPINBLOC1S4BLOC1S5LYST
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q969F9
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.68LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.54 [0.42–0.68]
RankingsWhere HPS3 stands among ~20K protein-coding genes
  • #10,183of 20,598
    Most Researched40
  • #223of 5,498
    Most Pathogenic Variants280 Β· top 5%
  • #5,124of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedHPS3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Hermansky-Pudlak syndrome: Mutation update.
PMID: 31898847
Hum Mutat Β· 2020
1.00
2
PMID: 20301464
0.90
3
Oculocutaneous albinism and bleeding diathesis due to a novel deletion in the
PMID: 36046236
Front Genet Β· 2022
0.80
4
Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease.
PMID: 28847206
N Engl J Med Β· 2017
0.70
5
A zinc transporter, transmembrane protein 163, is critical for the biogenesis of platelet dense granules.
PMID: 33513603
Blood Β· 2021
0.60